The next-generation sequencing reveals the complete mitochondrial genome of <i>Alosa sapidissima</i> (Perciformes: Clupeidae) with phylogenetic consideration

Wang, Jing; Yu, Zeshu; Xiang, Wei; Yang, Shaosheng; Zhang, Dongguo; Zhang, Yong

doi:10.1080/23802359.2017.1331322

Cited by 6 publications

(1 citation statement)

References 5 publications

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“…Alosa sapidissima is well discussed among the alosines for its biological, nutritional, and commercial calibre [1][2][3][4]. Their native range from the North Atlantic coast extends to several freshwater tributaries where come to reproduce by migrating, sometimes up to 1800km upstream [5][6][7].…”

Section: Objectivementioning

confidence: 99%

First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima

Sarker

Huang

et al. 2022

Preprint

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Objectives: American shad (Alosa sapidissima) is an important migratory fish under Alosine and has long been valued for its economic, nutritional and cultural attributes. Overfishing and barriers across the passage made it vulnerable to sustain. To protect this valuable species, aquaculture action plans have been taken though there are no published genetic resources prevailing yet. So, here we reported a de novo transcriptome assembly and annotation for A. sapidissima from blood and brain tissues for the first time.Data description: We generated 160,481 and 129,040 non-redundant transcripts from brain and blood tissues. The entire work strategy involved RNA extraction, library preparation, sequencing, de novo assembly, filtering, annotation and validation. Both coding and non-coding transcripts were annotated against Swissprot and Pfam datasets. Nearly, 83% coding transcripts were functionally assigned. Protein clustering with clupeiform and non-clupeiform taxa revealed ~82% coding transcripts retained the orthologue relationship which improved confidence over annotation procedure. Hopefully, it can serve as an useful resource in future for the research community to elucidate molecular mechanisms for several key traits like migration which is fascinating in clupeiform shads.

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Section: Objectivementioning

confidence: 99%

First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima

Sarker

Huang

et al. 2022

Preprint

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Combined Illumina and Pacbio sequencing technology on transcriptome analysis reveals several key regulations during the early development of American shad (Alosa sapidissima)

ZhengYuan

Feng²,

Miao

et al. 2022

Aquaculture Reports

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The Problems of DNA-Barcoding the Shads of Genus Alosa (Alosidae) of the Ponto-Caspian Basin

Orlova,

Emelyanova,

Nebesikhina

et al. 2024

J. Ichthyol.

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Abstract— Numerous studies show that species identification of representatives of the genus Alosa using various genetic markers is often difficult and the search for more specific biomarkers is required. For the first time we analyzed polymorphism of COI gene fragment of mitochondrial DNA of two representatives of this genus (A. tanaica and A. kessleri), supplemented with new data on A. immaculata, from the waters of the Ponto-Caspian basin in comparative aspect with other representatives of the herring (Clupeoidea) genera Alosa, Clupea, Clupeonella, Sprattus, and Sardinops. The main result was the conclusion that within the genus Alosa, it is not possible to identify species using the marker used. On the one hand, specimens collected from morphologically distinct individuals and identified as different species have the same haplotypes. On the other hand, samples belonging to different species differ from each other by an insignificant number of nucleotide substitutions and do not form independent clades on the phylogram and haplotype network. This indicates the absence of genetic differentiation between the studied samples of herrings of genus Alosa into separate species and species groups when using DNA barcoding based on the COI gene. The reasons for such a phenomenon may be the following: (1) incorrect identification of species in catches, since shads (Alosidae) have high morphological flexibility and in many species, the main external morphological characters often overlap; (2) recent time of speciation by the standards of biological evolution for shads of genus Alosa; (3) difference in proportion of interspecific hybrids, which can vary significantly between populations of the same species.

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The next-generation sequencing reveals the complete mitochondrial genome of Alosa sapidissima (Perciformes: Clupeidae) with phylogenetic consideration

Abstract: (2017) The next-generation sequencing reveals the complete mitochondrial genome of Alosasapidissima (Perciformes: Clupeidae) with phylogenetic consideration, Mitochondrial DNA Part B, 2:1, 304-306,

Cited by 6 publications

References 5 publications

First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima

First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima

Combined Illumina and Pacbio sequencing technology on transcriptome analysis reveals several key regulations during the early development of American shad (Alosa sapidissima)

The Problems of DNA-Barcoding the Shads of Genus Alosa (Alosidae) of the Ponto-Caspian Basin

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